pQTLtools: A reference manual

In jinghuazhao/pQTLtools: A Protein Quantitative Trait Locus Toolkit

A reference manual

Description

It collects data and utilities for pQTL analysis, including 1. Protein GWAS facilities such as Manhattan/QQ/LocusZoom.js plots, novelty/consequence checking; 2. Articles linking functions for cis/trans classification, pQTL-gene plot, 2d/3d-plotly plots, forest plots among others available from gap, https://cran.r-project.org/package=gap, as well as colocalization, pQTL-Mendelian Randomization via TwoSampleMR. https://mrcieu.github.io/TwoSampleMR/; 3. Query on genes, regions, and SNPs via PhenoScanner, http://www.phenoscanner.medschl.cam.ac.uk/. 4. Mapping of UniProt IDs to other resources; 5. Showcases of Bioconductor, https://github.com/bioconductor, and snakemake, https://github.com/snakemake.

Details

Available data and functions are listed in the following table.

Objects	Description
GWAS
turboman	Manhattan plots
turboqq	QQ plots
pGWAS
csq	Variant consequence
novelty_check	Locus novelty check
peptideAssociationPlot	peptide association plot
peptideMapping	peptide-to-protein mapping
protein_altering_variants	Protein Altering Variants (PAVs)
Expression analysis
get.prop.below.LLOD	Limit of detection analysis
import_eQTLCatalogue	Import eQTL Catalogue
make_ExpressionSet	A call to ExpressionSet class
run_coloc	Colocalisation analysis
MR analysis
import_OpenGWAS	Import OpenGWAS
pqtlMR	Bidirectional pQTL-MR analysis
qtl_lookup	QTL lookup
run_TwoSampleMR	A generic wrapper for TwoSampleMR analysis
PhenoScanner Utilities
genequeries	phenoscanner genequeries in batches
regionqueries	phenoscanner regionqueries in batches
snpqueries	phenoscanner snpqueries in batches
UniProt API
uniprot2ids	UniProt ID to others
Functions in gap
gap::METAL_forestplot	Forest plots from metal analysis
gap::ci2ms	Effect size and standard error from confidence interval
gap::cis.vs.trans.classification	a cis/trans classifier
gap::circos.cis.vs.trans.plot	circos plot of cis/trans classification
gap::circos.mhtplot	circos Manhattan plot with gene annotation
gap::circos.mhtplot2	Another circos Manhattan plot
gap::cs	Credible set
gap::get_b_se	Get b and se from AF, n, and z
gap::get_pve_se	Get pve and its standard error from n, z
gap::get_sdy	Get sd(y) from AF, n, b, se
gap::mr	Mendelian randomization analysis
gap::invnormal	Inverse normal transformation
gap::log10p	log10(p) for a standard normal deviate
gap::log10pvalue	log10(p) for a P value including its scientific format
gap::logp	log(p) for a normal deviate
gap::mhtplot.trunc	Truncated Manhattan plot
gap::miamiplot2	Miami plot
gap::mr_forestplot	Mendelian Randomization forest plot
gap::pvalue	P value for a normal deviate
gap::qtlClassifier	A QTL cis/trans classifier
gap::qtlFinder	Distance-based signal identification
gap::qtl2dplot	2D QTL plot
gap::qtl2dplotly	2D QTL plotly
gap::qtl3dplotly	3D QTL plotly

Usage

Vignettes on package usage:

• An Overview of pQTLtools. vignette("pQTLtools").

• Bioconductor Notes. vignette("bioconductor").

• ExpressionSet/SummarizedExperiment usage. vignette("esse").

• LocusZoom.js. vignette("LocusZoom.js").

• snakemake showcases. vignette("snakemake").

• Spectrum data analysis. vignette("spectrum").

• SCALLOP-INF scripts. vignette("SCALLOP-INF").

Author(s)

Jing Hua Zhao in collaboration with other colleagues

See Also

Useful links:

• https://github.com/jinghuazhao/pQTLtools

• Report bugs at https://github.com/jinghuazhao/pQTLtools/issues

jinghuazhao/pQTLtools documentation built on Dec. 16, 2024, 3:44 p.m.